A new version of RxNES has been released, with speed increases and constant improvements and features.

RxNES is a nes emulator based on mynes, it uses the unity engine, which allows graphic mods, 2D and 3D, as well as sound and music mods.
Its still very much wip, but includes a sample mod for super mario bros::

Snes9x is a portable, freeware Super Nintendo Entertainment System (SNES) emulator. It basically allows you to play most games designed for the SNES and Super Famicom Nintendo game systems on your PC or Workstation; which includes some real gems that were only ever released in Japan.

Snes9x is the result of well over three years worth of part-time hacking, coding, recoding, debugging, divorce, etc. (just kidding about the divorce bit). Snes9x is coded in C++, with three assembler CPU emulation cores on the i386 Linux and Windows ports.
Currently there are many ports of Snes9x available, please check the download page to see if a port exists for your system.